Stable isotopic composition (δ18O and δD of water, δ13CDIC) of the water column in the open ocean is related to the origin of water masses. Due to the recently increase of paleoceanographic studies on continental shelves, it is also important to understand their distribution and variability in those systems. To examine the influence of continental shelves internal processes on isotopic composition of water masses, we present data of stable isotopes and phosphate content from a western boundary upwelling system located on the Southeastern Brazilian coast and compare them with offshore observations. High mixing of the main water masses (SSW, TW and SACW) was observed in the majority of the samples collected during different seasons in 2011 and 2012. A mixing triangle approach was used to separate the water masses contribution and characterize their isotopic composition. In addition, an isotopic three end-member model was established, proposing it as a paleoceanographic tool to reconstruct relative contribution of these water masses in sediment records. Variations of δ18O values are linked to oceanographic dynamics, mixing, continental runoff and upwelling processes on the shelf. Differently the δ13CDIC variations in the middle and inner part of the shelf are related to the productivity of the upwelling system. Seasonal variability of the δ13CDIC values may be also related to changes in the upwelling intensity.